From: Joaquim Rui de Castro Rodrigues (
Date: Mon Aug 20 2012 - 14:13:34 CDT

Dear VMD users,

I am trying to write a psf with the following commands:
mol new complex.pdb
set sel [atomselect top all]
$sel writepsf test1.psf

psfplugin) WARNING: PSF file is incomplete, no angles, dihedrals,
psfplugin) impropers, or cross-terms will be written.
Info) Opened coordinate file test1.psf for writing.
Info) Finished with coordinate file test1.psf.

However, the psf does not contains bonds.
Strangely, if I add a random bond with the mouse, and then delete it, VMD outputs all the bonds.

Is this expected? How can I force VMD to write bonds without having to add/delete a bond?

This is with VMD 1.9.1, on a Mac (OS X 10.5.8)
Rui Rodrigues